[2019-06-24 19:24:25] Beginning TopHat run (v2.1.1)
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[2019-06-24 19:24:25] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 19:24:26] Checking for Bowtie index files (genome)..
[2019-06-24 19:24:26] Checking for reference FASTA file
[2019-06-24 19:24:26] Generating SAM header for Bowtie2Index/genome
[2019-06-24 19:24:28] Reading known junctions from GTF file
[2019-06-24 19:24:32] Preparing reads
	 left reads: min. length=32, max. length=36, 16552882 kept reads (34175 discarded)
	right reads: min. length=32, max. length=36, 16408473 kept reads (178584 discarded)
[2019-06-24 19:30:46] Building transcriptome data files /scratch/7056793.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 19:31:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 19:36:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:45:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:53:29] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
	If the read length is greater than or equal to 45bp,
	we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2019-06-24 19:53:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:54:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:57:23] Searching for junctions via segment mapping
[2019-06-24 19:59:53] Retrieving sequences for splices
[2019-06-24 20:02:24] Indexing splices
[2019-06-24 20:02:36] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056793.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:02:39] Joining segment hits
[2019-06-24 20:06:22] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056793.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:06:24] Joining segment hits
[2019-06-24 20:10:34] Reporting output tracks
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[2019-06-24 20:53:17] A summary of the alignment counts can be found in /scratch/7056793.1.linga/tophat2/align_summary.txt
[2019-06-24 20:53:17] Run complete: 01:28:51 elapsed